Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities. - Van-Nui Nguyen; Kai-Yao Huang; Chien-Hsun Huang; Tzu-Hao Chang; Neil Arvin Bretaña; K. Robert Lai; Julia Weng; Tzong-Yi Lee (BMC Bioinform., 2015)

UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation. - Van-Nui Nguyen; Kai-Yao Huang; Julia Tzu-Ya Weng; K. Robert Lai; Tzong-Yi Lee (Database J. Biol. Databases Curation, 2016)

A New Scheme to Characterize and Identify Protein Ubiquitination Sites. - Van-Nui Nguyen; Kai-Yao Huang; Chien-Hsun Huang; K. Robert Lai; Tzong-Yi Lee (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

SNARE-CNN: a 2D convolutional neural network architecture to identify SNARE proteins from high-throughput sequencing data. - Nguyen-Quoc-Khanh Le; Van-Nui Nguyen (PeerJ Comput. Sci., 2019)

SuccSite: Incorporating Amino Acid Composition and Informative k-spaced Amino Acid Pairs to Identify Protein Succinylation Sites. - Hui-Ju Kao; Van-Nui Nguyen; Kai-Yao Huang; Wen-Chi Chang; Tzong-Yi Lee (Genom. Proteom. Bioinform., 2020)

BERT-Promoter: An improved sequence-based predictor of DNA promoter using BERT pre-trained model and SHAP feature selection. - Nguyen-Quoc-Khanh Le; Quang-Thai Ho; Van-Nui Nguyen; Jung-Su Chang (Comput. Biol. Chem., 2022)

Enhancing Protein Sequence Classification with a Fuzzy Neural Network: A Study in Anticancer Peptide Identification. - Nguyen Quoc Khanh Le; Van-Nui Nguyen; Thi-Tuyen Nguyen; Thi-Xuan Tran; Trang-Thi Ho (iFUZZY, 2024)

Using a hybrid neural network architecture for DNA sequence representation: A study on N4-methylcytosine sites. - Van-Nui Nguyen; Trang-Thi Ho; Thu-Dung Doan; Nguyen-Quoc-Khanh Le (Comput. Biol. Medicine, 2024)

Integrating CNN and Bi-LSTM for protein succinylation sites prediction based on Natural Language Processing technique. - Thi-Xuan Tran; Nguyen Quoc Khanh Le; Van-Nui Nguyen (Comput. Biol. Medicine, 2025)